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MannLabs / alphamap

An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge.
https://mannlabs.github.io/alphamap/
Apache License 2.0
76 stars 18 forks source link

MSFragger / FragPipe integration #23

Closed hcadre closed 3 years ago

hcadre commented 3 years ago

It would be very helpful to also have the possibility to upload results from a search performed with FragPipe (combined_peptide.tsv?). Thank you for this tool!

ibludau commented 3 years ago

Thanks for the suggestion to include FragPipe output. We're still expanding on the input formats and can certainly aim to incorporate that for the next release!

hcadre commented 3 years ago

Purrfect! Thanks!

ibludau commented 3 years ago

Hey, could you maybe share an example combined_peptide.tsv with us so we can look into the integration? We would only need a handful of proteins including some PTMs.

hcadre commented 3 years ago

Enclosed, please find excerpts from the combined_peptide.tsv as well as from the combined_protein.tsv files. Hope this helps! combined_protein_alphamap.txt combined_peptide_alphamap.txt

ibludau commented 3 years ago

Thanks a lot for providing the example files. I realised that the site positions of observed PTMs are not annotated in the sequence. Is there an additional output file that contains this information? Otherwise AlphaMap cannot show them.

hcadre commented 3 years ago

Oh yes, I should have known better: Unfortunately, FragPipe / MSFRagger currently does not provide PTM positional information on the protein level. According to Alexey Nesvizhskii this is due to Philosopher, which does not generate site-level reports and that there is a need for parsers / tools that would do the job. Fragpipe however generates a peptide.tsv file per each raw file, which contains information about the position of a PTM relative to the sequence of the peptide, in which the PTM is present. But that would not help a lot, would it? I attach an example anyway. peptide_alphamap.txt

ibludau commented 3 years ago

This table actually contains the necessary information, but this means that you could only upload single runs at a time I assume? That is slightly suboptimal. Options are therefore the following:

  1. enable combined_peptide.tsv as input format and ​and neglect PTM information at this point
  2. enable the peptide.tsv file import for individual runs including PTM information (but being limited to a single run per trace)

Do you have a preference for your applications?

EugeniaVoytik commented 3 years ago

Thank you for suggesting this feature! We've integrated two options that Isabell mentioned in the previous comment. You may read more about it in the instructions for the import of FragPipe output files in AlphaMap in GUI directly or in the README.md file.